From 618d4236beff849e36b4b9919406eac5df606436 Mon Sep 17 00:00:00 2001
From: mmassaviol <mathieu.massaviol@hotmail.fr>
Date: Fri, 13 Dec 2019 14:44:24 +0100
Subject: [PATCH] Update deseq2 script (get back to basic use)
---
Dockerfile | 3 +++
files/params.total.yml | 13 -------------
files/scripts/deseq2.script.R | 2 +-
files/singularity.def | 16 ++++++++++++++--
install.sh | 11 +++++++++--
sagApp/pages/pages_def_de.R | 4 ----
sagApp/server/opt_global.R | 12 ------------
waw_workflow.qsub | 2 +-
8 files changed, 28 insertions(+), 35 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 8bad83c..6b31fce 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -42,6 +42,9 @@ RUN Rscript -e 'BiocManager::install("apeglm", version = "3.8",Ncpus=8, clean=TR
RUN Rscript -e 'BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, clean=TRUE)'
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8
#This part is necessary to run on ISEM cluster
RUN mkdir -p /share/apps/lib \
diff --git a/files/params.total.yml b/files/params.total.yml
index 93aa4f8..c40a780 100644
--- a/files/params.total.yml
+++ b/files/params.total.yml
@@ -48,8 +48,6 @@ params:
deseq2_tx2gene: false
deseq2_annotations_select: server
deseq2_annotations: ''
- deseq2_fitType: parametric
- deseq2_betaPrior: false
samples: []
groups: []
steps:
@@ -211,17 +209,6 @@ params_info:
rule: deseq2
type: input_file
label: 'Annotation file (gtf or gff) : '
- deseq2_fitType:
- tool: deseq2
- rule: deseq2
- type: radio
- label: Type of fitting of dispersions to the mean intensity
- deseq2_betaPrior:
- tool: deseq2
- rule: deseq2
- type: checkbox
- label: 'betaPrior: whether or not to put a zero-mean normal prior on the non-intercept
- coefficients.'
prepare_report_scripts: []
prepare_report_outputs: {}
outputs:
diff --git a/files/scripts/deseq2.script.R b/files/scripts/deseq2.script.R
index bb507ba..705bbf0 100644
--- a/files/scripts/deseq2.script.R
+++ b/files/scripts/deseq2.script.R
@@ -42,7 +42,7 @@ dds <- dds[keep,]
dds$condition <- factor(dds$condition, levels = unique(conditions))
-dds <- DESeq(dds, fitType = snakemake@config[["deseq2_fitType"]], betaPrior = as.logical(snakemake@config[["deseq2_betaPrior"]]), test="Wald")
+dds <- DESeq(dds) #, fitType = snakemake@config[["deseq2_fitType"]], betaPrior = as.logical(snakemake@config[["deseq2_betaPrior"]]), test="Wald")
res <- results(dds)
diff --git a/files/singularity.def b/files/singularity.def
index b5c1338..6ab135b 100644
--- a/files/singularity.def
+++ b/files/singularity.def
@@ -5,8 +5,9 @@ From: ../base.sif
export PATH=/opt/biotools/bin:$PATH
export ROOTSYS=/opt/biotools/root
export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'
-
-
+ export LANG=en_US.UTF-8
+export LANGUAGE=en_US:en
+export LC_ALL=en_US.UTF-8
%labels
Author YourName
@@ -120,3 +121,14 @@ singularity run --app appName this_container.sif
Rscript -e 'BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, clean=TRUE)'
+mkdir -p /share/apps/bin
+mkdir /share/apps/lib
+mkdir /share/apps/gridengine
+mkdir /share/bio
+mkdir -p /opt/gridengine
+mkdir -p /export/scrach
+mkdir -p /usr/lib64
+ln -s /bin/bash /bin/mbb_bash
+ln -s /bin/bash /bin/isem_bash
+/usr/sbin/groupadd --system --gid 400 sge
+/usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
\ No newline at end of file
diff --git a/install.sh b/install.sh
index d60ff7d..09ebbc4 100644
--- a/install.sh
+++ b/install.sh
@@ -1,2 +1,9 @@
-##### nginx install #####
-sudo apt-get install -y nginx
+#!/bin/bash
+
+sudo apt-get update
+
+##### Docker install #####
+sudo apt-get install -y docker.io
+
+##### nginx install #####
+sudo apt-get install -y nginx
\ No newline at end of file
diff --git a/sagApp/pages/pages_def_de.R b/sagApp/pages/pages_def_de.R
index 498cb75..8e41da1 100644
--- a/sagApp/pages/pages_def_de.R
+++ b/sagApp/pages/pages_def_de.R
@@ -60,10 +60,6 @@ conditionalPanel(condition = "input.selectDE == 'deseq2'",box(title = "DESeq2",
)
,
- radioButtons("deseq2_fitType", label = "Type of fitting of dispersions to the mean intensity", choices = list("parametric" = "parametric", "local" = "local", "mean" = "mean"), selected = "parametric", width = "auto"),
-
- checkboxInput("deseq2_betaPrior", label = "betaPrior: whether or not to put a zero-mean normal prior on the non-intercept coefficients.", value = FALSE),
-
p("DESeq2: Differential gene expression analysis based on the negative binomial distribution. Using normalized count data."),
p("Website : ",a(href="https://bioconductor.org/packages/release/bioc/html/DESeq2.html","https://bioconductor.org/packages/release/bioc/html/DESeq2.html",target="_blank")),
diff --git a/sagApp/server/opt_global.R b/sagApp/server/opt_global.R
index 286e7a9..fe01db3 100644
--- a/sagApp/server/opt_global.R
+++ b/sagApp/server/opt_global.R
@@ -169,18 +169,6 @@ save_params <- function(path_param){
res = paste0(res, paste("deseq2_annotations:", paste0('"', input$deseq2_annotations_local$datapath, '"'), "\n", sep = " "))
}
- if(!is.na(as.numeric(input$deseq2_fitType))) {
- res = paste0(res, paste("deseq2_fitType:", input$deseq2_fitType, "\n", sep = " "))
- } else {
- res = paste0(res, paste("deseq2_fitType:", paste0('"', input$deseq2_fitType, '"'), "\n", sep = " "))
- }
-
- if(input$deseq2_betaPrior) {
- res = paste0(res, paste("deseq2_betaPrior:", "true", "\n", sep = " "))
- } else {
- res = paste0(res, paste("deseq2_betaPrior:", "false", "\n", sep = " "))
- }
-
a = yaml.load_file("/workflow/params.total.yml")
p = a[["params"]]
a["params"] = NULL
diff --git a/waw_workflow.qsub b/waw_workflow.qsub
index 8801856..50bc865 100644
--- a/waw_workflow.qsub
+++ b/waw_workflow.qsub
@@ -21,7 +21,7 @@ configFile=$3
cores=$4
#if we must build the image from docker image
-singularity build rnaseqde.simg docker://mbbteam/rnaseqde:latest
+singularity build rnaseqde.simg docker://mbbteam/rnaseqde:latest
#Run the workflow in cmd line
--
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